Mercurial > repos > clustalomega > clustalomega
annotate clustalomega/clustal-omega-0.2.0/src/clustal-omega.h @ 0:ff1768533a07
Migrated tool version 0.2 from old tool shed archive to new tool shed repository
author | clustalomega |
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date | Tue, 07 Jun 2011 17:04:25 -0400 |
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1 /* -*- mode: c; tab-width: 4; c-basic-offset: 4; indent-tabs-mode: nil -*- */ |
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2 |
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3 /********************************************************************* |
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4 * Clustal Omega - Multiple sequence alignment |
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5 * |
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6 * Copyright (C) 2010 University College Dublin |
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7 * |
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8 * Clustal-Omega is free software; you can redistribute it and/or |
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9 * modify it under the terms of the GNU General Public License as |
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10 * published by the Free Software Foundation; either version 2 of the |
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11 * License, or (at your option) any later version. |
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12 * |
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13 * This file is part of Clustal-Omega. |
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14 * |
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15 ********************************************************************/ |
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16 |
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17 /* |
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18 * RCS $Id: clustal-omega.h 212 2011-03-10 15:09:46Z andreas $ |
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19 */ |
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20 |
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21 #ifndef CLUSTALO_H |
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22 #define CLUSTALO_H |
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23 |
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24 |
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25 |
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26 #ifdef HAVE_OPENMP |
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27 #include <omp.h> |
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28 #endif |
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29 |
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30 #include "clustal-omega-config.h" |
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31 |
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32 /* the following needs to be kept in sync with library_include_HEADERS of all |
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33 * subdir Makefile.am's |
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34 */ |
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35 |
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36 /* hhalign */ |
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37 #include "hhalign/general.h" |
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38 #include "hhalign/hhfunc.h" |
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39 |
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40 |
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41 /* clustal */ |
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42 #include "clustal/log.h" |
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43 #include "clustal/util.h" |
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44 #include "clustal/symmatrix.h" |
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45 #include "clustal/tree.h" |
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46 #include "clustal/seq.h" |
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47 #include "clustal/mbed.h" |
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48 #include "clustal/weights.h" |
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49 #include "clustal/pair_dist.h" |
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50 #include "clustal/hhalign_wrapper.h" |
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51 |
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52 |
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53 |
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54 #define CLUSTERING_UNKNOWN 0 |
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55 #define CLUSTERING_UPGMA 1 |
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56 |
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57 /* weights will be computed if 1. but are not really used for now and they |
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58 * might slow things down. also, mbed's screws up branch lengths which will |
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59 * have a negative effect on weights |
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60 */ |
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61 #define USE_WEIGHTS 0 |
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62 |
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63 extern int iNumberOfThreads; |
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64 |
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65 |
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66 /** user/commandline options |
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67 * |
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68 * changes here will have to be reflected in ParseCommandLine() |
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69 * and during setup of the default opts |
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70 * |
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71 */ |
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72 typedef struct { |
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73 /* auto: Clustal (know what) is good for you |
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74 */ |
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75 bool bAutoOptions; |
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76 |
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77 /* Distance matrix |
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78 */ |
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79 /** distance matrix input file */ |
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80 char *pcDistmatInfile; |
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81 /** distance matrix output file */ |
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82 char *pcDistmatOutfile; |
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83 |
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84 /* Clustering / guide-tree |
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85 */ |
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86 /** clustering type (from cmdline arg) */ |
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87 int iClusteringType; |
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88 /** pairwise distance method */ |
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89 int iPairDistType; |
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90 /** use mbed-like clustering */ |
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91 bool bUseMbed; |
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92 /** use mbed-like clustering also during iteration */ |
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93 bool bUseMbedForIteration; |
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94 /** guidetree output file */ |
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95 char *pcGuidetreeOutfile; |
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96 /** guidetree input file */ |
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97 char *pcGuidetreeInfile; |
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98 |
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99 /* HMMs |
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100 */ |
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101 /** HMM input files. index range: 0..iHMMInputFiles */ |
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102 char **ppcHMMInput; |
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103 /** number of provided HMM input files. not really a user |
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104 option but need for ppcHMMInput */ |
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105 int iHMMInputFiles; |
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106 |
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107 /* Iteration |
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108 */ |
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109 /** number of iterations */ |
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110 int iNumIterations; |
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111 /** determine number of iterations automatically */ |
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112 bool bIterationsAuto; |
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113 /** maximum number of hmm iterations */ |
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114 int iMaxHMMIterations; |
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115 /** max number of guidetree iterations */ |
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116 int iMaxGuidetreeIterations; |
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117 |
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118 /** max MAC RAM (maximum amount of RAM set aside for MAC algorithm) */ |
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119 int iMacRam; /* FS, r240 -> */ |
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120 |
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121 /* changes here will have to be reflected in FreeAlnOpts(), |
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122 * SetDefaultAlnOpts(), AlnOptsLogicCheck() etc |
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123 */ |
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124 } opts_t; |
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125 |
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126 |
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127 |
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128 |
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129 |
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130 extern void |
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131 PrintLongVersion(char *pcStr, int iSize); |
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132 |
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133 extern void |
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134 SetDefaultAlnOpts(opts_t *opts); |
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135 |
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136 extern void |
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137 FreeAlnOpts(opts_t *aln_opts); |
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138 |
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139 extern void |
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140 AlnOptsLogicCheck(opts_t *opts); |
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141 |
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142 extern void |
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143 PrintAlnOpts(FILE *prFile, opts_t *opts); |
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144 |
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145 extern void |
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146 InitClustalOmega(int iNumThreadsToUse); |
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147 |
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148 extern void |
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149 SequentialAlignmentOrder(int **piOrderLR_p, int iNumSeq); |
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150 |
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151 extern int |
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152 AlignmentOrder(int **piOrderLR_p, double **pdSeqWeights_p, mseq_t *prMSeq, |
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153 int iPairDistType, char *pcDistmatInfile, char *pcDistmatOutfile, |
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154 int iClusteringType, char *pcGuidetreeInfile, char *pcGuidetreeOutfile, |
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155 bool bUseMBed); |
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156 |
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157 extern int |
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158 Align(mseq_t *prMSeq, |
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159 mseq_t *prMSeqProfile, |
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160 opts_t *prOpts, |
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161 hhalign_para rHhalignPara); |
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162 |
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163 extern int |
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164 AlignProfiles(mseq_t *prMSeqProfile1, |
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165 mseq_t *prMSeqProfile2, hhalign_para rHhalignPara); |
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166 |
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167 #endif |